A case-control study was conducted in 140 people with histology proven cutaneous squamous cell carcinoma (SCC) and 454 controls, nested within 2 cohorts of organ transplant recipients (OTR) recruited in London and Oxford between 2002 and 2006. All participants had a skin examination, completed a questionnaire and had serum tested for antibodies against the L1 antigen of 34 HPV types using Luminex technology. SCC was more common in men than women (odds ratio [OR] = 1.7, 95% confidence interval [CI]: 1.1-2.8, p = 0.02) and in people with susceptibility to burn easily (OR = 3.0, 95%CI: 1.9-4.8; p < 0.001). The risk increased with increasing age (p-trend < 0.001), increasing time since transplant (p-trend < 0.001), increasing self-reported number of sunburns as a child (p-trend < 0.001) and with the presence of viral warts (p < 0.001). As expected, antibodies against HPV 16 were associated with a self-reported history of an abnormal cervical smear among women (OR 5.1, 95%CI: 2.6-10.2) and antibodies against HPV 6 were associated with a self-reported history of genital warts (OR 4.0, 95%CI: 2.2-7.2). However, no clear associations between any of the HPV types examined (including cutaneous betaHPVs) and SCC were identified. For example, the seroprevalence of HPV 5 was 15% among cases and 9% among controls (p = 0.09) and the seroprevalence of HPV 8 was 23% among cases and 21% among controls (p = 0.6). Nor was seropositivity to multiple types associated with SCC. These serological data do not provide evidence for a role for HPV in the aetiology of cutaneous SCC among OTR in two UK-based populations.